USB with data partition

Hi, Using Knoppix 6.6 from Linux magazine. I made a usb stick using the tool on the dvd. It boots okay and I can write things into the data partition from my DebMint machine.Issue 1chmod fails to do anything, right click a file properties/permissions fails to change permissions. I had to put the usb stick into my DebMint to do the job, w, r and x that is and x did run the program.Issue 2Reboot the usb Knoppix and with the r, w and x permissions set, r and w were okay but I could not run my program? sudo etc failed to help. Any hints please on running a program in the data partition? Regards Ian.